Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007515.1 Corchorus capsularis cultivar CVL-1 contig07536, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19907
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Found at i:788 original size:28 final size:28
Alignment explanation
Indices: 744--816 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
734 GTAGATTAAG
**
744 AATGACCAAAACACCCCCTAAATGCAAA
1 AATGACCAAAATGCCCCCTAAATGCAAA
* **
772 AATGACCAAAATGCCCCCTATATGTGAA
1 AATGACCAAAATGCCCCCTAAATGCAAA
800 AATGACCAAAATGCCCC
1 AATGACCAAAATGCCCC
817 TGAATGACCC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.44, C:0.30, G:0.11, T:0.15
Consensus pattern (28 bp):
AATGACCAAAATGCCCCCTAAATGCAAA
Found at i:1155 original size:45 final size:45
Alignment explanation
Indices: 1053--1251 Score: 229
Period size: 45 Copynumber: 4.4 Consensus size: 45
1043 AAGAGAGTAG
* * * * *
1053 TCTGTGGTCGACTTTGATAACTGCTG-AAAGTGAAAAAGATCTGT
1 TCTGAGGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGT
* *
1097 TCTGAGGTCAACTTTGATAACTACTGAAAACTGAGAAATACCTGT
1 TCTGAGGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGT
* * *
1142 TCTGAGGTCAACTTTGATAATTTCTGAAAACTGAGAAAGACATGT
1 TCTGAGGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGT
* * * * *
1187 TCTGCGGTCAACTTTGATAACTGTTGAAAACTGTGAAAGACTTAT
1 TCTGAGGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGT
* * *
1232 TTTGGGGTCGACTTTGATAA
1 TCTGAGGTCAACTTTGATAA
1252 TCTTATTGAA
Statistics
Matches: 133, Mismatches: 21, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
44 23 0.17
45 110 0.83
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.32
Consensus pattern (45 bp):
TCTGAGGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGT
Found at i:2685 original size:14 final size:14
Alignment explanation
Indices: 2662--2702 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2652 ACCCTACAGC
*
2662 TTCTTCTTCTTTTT
1 TTCTTTTTCTTTTT
2676 TTCTTTTTCTTTTT
1 TTCTTTTTCTTTTT
*
2690 TCTTTTTTTCTTT
1 T-TCTTTTTCTTT
2703 CTCCTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTTTTTCTTTTT
Found at i:2694 original size:21 final size:22
Alignment explanation
Indices: 2668--2712 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
2658 CAGCTTCTTC
*
2668 TTCTTTTTTTCTTT-TTCTTTT
1 TTCTTTTTTTCTTTCTCCTTTT
2689 TTCTTTTTTTCTTTCTCCTTTT
1 TTCTTTTTTTCTTTCTCCTTTT
2711 TT
1 TT
2713 TTATTATGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (22 bp):
TTCTTTTTTTCTTTCTCCTTTT
Found at i:2697 original size:15 final size:15
Alignment explanation
Indices: 2668--2713 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2658 CAGCTTCTTC
*
2668 TTCTTTTTT-TCTTT
1 TTCTTTTTTCTTTTT
2682 TTCTTTTTTCTTTTT
1 TTCTTTTTTCTTTTT
* *
2697 TTCTTTCTCCTTTTT
1 TTCTTTTTTCTTTTT
2712 TT
1 TT
2714 TATTATGCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 9 0.32
15 19 0.68
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTCTTTTTTCTTTTT
Found at i:3984 original size:14 final size:13
Alignment explanation
Indices: 3965--4008 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
3955 ACTCAAAACC
3965 TTTTGAAAACTCAT
1 TTTTGAAAAC-CAT
*
3979 TTTTGAAAACCTT
1 TTTTGAAAACCAT
3992 TTCTTGAAAA-CAT
1 TT-TTGAAAACCAT
4005 TTTT
1 TTTT
4009 TTTTTGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 2 0.07
13 8 0.30
14 17 0.63
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.48
Consensus pattern (13 bp):
TTTTGAAAACCAT
Found at i:5186 original size:42 final size:41
Alignment explanation
Indices: 5132--5241 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 41
5122 ACAAGTGATA
* * * * *
5132 GCATGATGGATGCATGAGCATATATACTAATGA-ATGGATAGT
1 GCATGAT-GATGCATAAACATATATAC-AAAGAGATGGACAAT
5174 GCATGATCGATGCATAAACATATATACAAAGAGATGGACAAT
1 GCATGAT-GATGCATAAACATATATACAAAGAGATGGACAAT
5216 GCATGATGAATGCAT---CATATATACAA
1 GCATGATG-ATGCATAAACATATATACAA
5242 GTGACTGACT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
39 11 0.18
41 5 0.08
42 44 0.73
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (41 bp):
GCATGATGATGCATAAACATATATACAAAGAGATGGACAAT
Found at i:6726 original size:25 final size:24
Alignment explanation
Indices: 6693--6818 Score: 105
Period size: 24 Copynumber: 5.2 Consensus size: 24
6683 TAATTATTCT
6693 CTTTT-TACTGATTACCATTTTTA
1 CTTTTCTACTGATTACCATTTTTA
* *
6716 CTTTTGCTACT-TTTATCATTTTTA
1 CTTTT-CTACTGATTACCATTTTTA
* **
6740 CCTTTT-TACTGAATGTCATTTTTA
1 -CTTTTCTACTGATTACCATTTTTA
* *
6764 CTCTTTTTACTGAATACCATTTTTA
1 CT-TTTCTACTGATTACCATTTTTA
* *
6789 TTCTTTTCTACTGATTGCCATTTTCA
1 --CTTTTCTACTGATTACCATTTTTA
6815 CTTT
1 CTTT
6819 ACTAATTACT
Statistics
Matches: 84, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
23 11 0.13
24 28 0.33
25 25 0.30
26 18 0.21
27 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (24 bp):
CTTTTCTACTGATTACCATTTTTA
Found at i:6749 original size:48 final size:49
Alignment explanation
Indices: 6693--6818 Score: 130
Period size: 48 Copynumber: 2.6 Consensus size: 49
6683 TAATTATTCT
* ** *
6693 CTTTTTACTGATTACCATTTTTACTTTTGCTACT-TTTATCATTTTTA-C
1 CTTTTTACTGATTGCCATTTTTACTTTT-CTACTGAATACCATTTTTATC
* * * *
6741 CTTTTTACTGAATGTCATTTTTACTCTTTTTACTGAATACCATTTTTATT
1 CTTTTTACTGATTGCCATTTTTACT-TTTCTACTGAATACCATTTTTATC
*
6791 CTTTTCTACTGATTGCCATTTTCACTTT
1 CTTTT-TACTGATTGCCATTTTTACTTT
6819 ACTAATTACT
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
48 26 0.41
49 13 0.21
50 7 0.11
51 17 0.27
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (49 bp):
CTTTTTACTGATTGCCATTTTTACTTTTCTACTGAATACCATTTTTATC
Found at i:6771 original size:26 final size:25
Alignment explanation
Indices: 6732--6812 Score: 110
Period size: 25 Copynumber: 3.2 Consensus size: 25
6722 CTACTTTTAT
*
6732 CATTTTTAC-CTTTTTACTGAATGT
1 CATTTTTACTCTTTTTACTGAATGC
*
6756 CATTTTTACTCTTTTTACTGAATAC
1 CATTTTTACTCTTTTTACTGAATGC
* *
6781 CATTTTTATTCTTTTCTACTGATTGC
1 CATTTTTACTCTTTT-TACTGAATGC
6807 CATTTT
1 CATTTT
6813 CACTTTACTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
24 9 0.18
25 27 0.54
26 14 0.28
ACGTcount: A:0.20, C:0.19, G:0.06, T:0.56
Consensus pattern (25 bp):
CATTTTTACTCTTTTTACTGAATGC
Found at i:6818 original size:24 final size:23
Alignment explanation
Indices: 6693--6818 Score: 101
Period size: 25 Copynumber: 5.2 Consensus size: 23
6683 TAATTATTCT
6693 CTTTTTACTGATTACCATTTTTA
1 CTTTTTACTGATTACCATTTTTA
* *
6716 CTTTTGCTACT-TTTATCATTTTTA
1 CTTTT--TACTGATTACCATTTTTA
* **
6740 CCTTTTTACTGAATGTCATTTTTA
1 -CTTTTTACTGATTACCATTTTTA
*
6764 CTCTTTTTACTGAATACCATTTTTA
1 --CTTTTTACTGATTACCATTTTTA
* *
6789 TTCTTTTCTACTGATTGCCATTTTCA
1 --CTTTT-TACTGATTACCATTTTTA
6815 CTTT
1 CTTT
6819 ACTAATTACT
Statistics
Matches: 85, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
23 9 0.11
24 25 0.29
25 36 0.42
26 15 0.18
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (23 bp):
CTTTTTACTGATTACCATTTTTA
Found at i:6863 original size:36 final size:36
Alignment explanation
Indices: 6806--7506 Score: 557
Period size: 36 Copynumber: 18.9 Consensus size: 36
6796 CTACTGATTG
* * *
6806 CCATTTT-CACTTTACTAATTACTATTTACTCTTTA
1 CCATTTTACTCTTTACTGATTACTCTTTACTCTTTA
* * *
6841 CCATTTTGCTTTTTACTGATTACTCTTTACTTTTTTA
1 CCATTTTACTCTTTACTGATTACTCTTTAC-TCTTTA
*
6878 CCATTTTACCCTTTACTGATTACTCTTTACTCTTTA
1 CCATTTTACTCTTTACTGATTACTCTTTACTCTTTA
* * * ** * *
6914 CTA-ATTACTATTTTACTCTCTTGAATTTAATTAC-CATTTTA
1 CCATTTTACT-CTTTACT-GATT-ACTCT--TTACTC--TTTA
*
6955 CCATTTTTCTCTTTACTGATTACTCTTTACT-TTTA
1 CCATTTTACTCTTTACTGATTACTCTTTACTCTTTA
* * ** * *
6990 AC-TCTTTACTATTTTACTCTCTTGAATTTAATTAC-CATTTTA
1 CCAT-TTTACT-CTTTACT-GATT-ACTCT--TTACTC--TTTA
*
7032 CCATTTTTCTCTTTACTGATTACTCTTTACTCTTTA
1 CCATTTTACTCTTTACTGATTACTCTTTACTCTTTA
* *
7068 CTCTTTACTCTTTTCTCTTTACTGATTACTCTATACTCTTTA
1 C-C---A-T-TTTACTCTTTACTGATTACTCTTTACTCTTTA
* * *
7110 -CACTTTT-CTCTTTACTGATTACTATATACTGTTTA
1 CCA-TTTTACTCTTTACTGATTACTCTTTACTCTTTA
*
7145 CCATTTTCCTCTTTACTGATTACTCTTTAC-CTTTTA
1 CCATTTTACTCTTTACTGATTACTCTTTACTC-TTTA
*
7181 CCATTTTACTCTTTACTGATTACTCTTTACTTTTTA
1 CCATTTTACTCTTTACTGATTACTCTTTACTCTTTA
* *
7217 CCATTTTACCCTTTACTGATTACTTTTTACTCTTTA
1 CCATTTTACTCTTTACTGATTACTCTTTACTCTTTA
* * * ** * *
7253 CTA-ATTACTATTTTACTCTCTTGAATTTAATTAC-CATTTTA
1 CCATTTTACT-CTTTACT-GATT-ACTCT--TTACTC--TTTA
* *
7294 CCATTTTTCTCTTTACTGATTACTCTATACTCTTTA
1 CCATTTTACTCTTTACTGATTACTCTTTACTCTTTA
* *
7330 CTC-TTTT-CTCTTTACTGATAACTCTATACTCTTTA
1 C-CATTTTACTCTTTACTGATTACTCTTTACTCTTTA
* * *
7365 CCATTTTCCTCTTTACTGTTTACTCTTTACTTTTTA
1 CCATTTTACTCTTTACTGATTACTCTTTACTCTTTA
*
7401 CCATTTTACTCTTTACTGATTACTCTTTACTTTTTA
1 CCATTTTACTCTTTACTGATTACTCTTTACTCTTTA
7437 CCATTTTACTCTTTACTGATTACTCTTTACTCTTTA
1 CCATTTTACTCTTTACTGATTACTCTTTACTCTTTA
* * *
7473 CTC-TTTTTCTCTTTACTAATTACTATTTTACTCT
1 C-CATTTTACTCTTTACTGATTACT-CTTTACTCT
7507 CTTGATTTTA
Statistics
Matches: 543, Mismatches: 77, Indels: 90
0.76 0.11 0.13
Matches are distributed among these distances:
34 2 0.00
35 87 0.16
36 267 0.49
37 63 0.12
38 12 0.02
39 11 0.02
40 20 0.04
41 31 0.06
42 49 0.09
43 1 0.00
ACGTcount: A:0.20, C:0.23, G:0.03, T:0.54
Consensus pattern (36 bp):
CCATTTTACTCTTTACTGATTACTCTTTACTCTTTA
Found at i:6982 original size:14 final size:14
Alignment explanation
Indices: 6963--7002 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
6953 TACCATTTTT
6963 CTCTTTACTGATT-A
1 CTCTTTACT-ATTAA
*
6977 CTCTTTACTTTTAA
1 CTCTTTACTATTAA
6991 CTCTTTACTATT
1 CTCTTTACTATT
7003 TTACTCTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.20, C:0.23, G:0.03, T:0.55
Consensus pattern (14 bp):
CTCTTTACTATTAA
Found at i:7061 original size:7 final size:7
Alignment explanation
Indices: 7040--7489 Score: 216
Period size: 7 Copynumber: 62.3 Consensus size: 7
7030 TACCATTTTT
7040 CTCTTTA
1 CTCTTTA
**
7047 CTGATTA
1 CTCTTTA
7054 CTCTTTA
1 CTCTTTA
7061 CTCTTTA
1 CTCTTTA
7068 CTCTTTA
1 CTCTTTA
*
7075 CTCTTTT
1 CTCTTTA
7082 CTCTTTA
1 CTCTTTA
**
7089 CTGATTA
1 CTCTTTA
*
7096 CTCTATA
1 CTCTTTA
7103 CTCTTTA
1 CTCTTTA
* *
7110 CACTTTT
1 CTCTTTA
7117 CTCTTTA
1 CTCTTTA
**
7124 CTGATTA
1 CTCTTTA
* *
7131 CTATATA
1 CTCTTTA
*
7138 CTGTTTA
1 CTCTTTA
*
7145 C-CATTTTC
1 CTC--TTTA
7153 CTCTTTA
1 CTCTTTA
**
7160 CTGATTA
1 CTCTTTA
7167 CTCTTTA
1 CTCTTTA
7174 C-CTTTTA
1 CTC-TTTA
7181 C-CATTTTA
1 CTC--TTTA
7189 CTCTTTA
1 CTCTTTA
**
7196 CTGATTA
1 CTCTTTA
7203 CTCTTTA
1 CTCTTTA
*
7210 CTTTTTA
1 CTCTTTA
7217 C-CATTTTA
1 CTC--TTTA
*
7225 CCCTTTA
1 CTCTTTA
**
7232 CTGATTA
1 CTCTTTA
*
7239 CTTTTTA
1 CTCTTTA
7246 CTCTTTA
1 CTCTTTA
**
7253 CTAATTA
1 CTCTTTA
*
7260 CTATTTTA
1 CT-CTTTA
7268 CTCTCTTGA
1 CTCT-TT-A
* *
7277 ATTTAATTA
1 CTCT--TTA
7286 C-CATTTTA
1 CTC--TTTA
*
7294 C-CATTTTT
1 CTC--TTTA
7302 CTCTTTA
1 CTCTTTA
**
7309 CTGATTA
1 CTCTTTA
*
7316 CTCTATA
1 CTCTTTA
7323 CTCTTTA
1 CTCTTTA
*
7330 CTCTTTT
1 CTCTTTA
7337 CTCTTTA
1 CTCTTTA
** *
7344 CTGATAA
1 CTCTTTA
*
7351 CTCTATA
1 CTCTTTA
7358 CTCTTTA
1 CTCTTTA
*
7365 C-CATTTTC
1 CTC--TTTA
7373 CTCTTTA
1 CTCTTTA
*
7380 CTGTTTA
1 CTCTTTA
7387 CTCTTTA
1 CTCTTTA
*
7394 CTTTTTA
1 CTCTTTA
7401 C-CATTTTA
1 CTC--TTTA
7409 CTCTTTA
1 CTCTTTA
**
7416 CTGATTA
1 CTCTTTA
7423 CTCTTTA
1 CTCTTTA
*
7430 CTTTTTA
1 CTCTTTA
7437 C-CATTTTA
1 CTC--TTTA
7445 CTCTTTA
1 CTCTTTA
**
7452 CTGATTA
1 CTCTTTA
7459 CTCTTTA
1 CTCTTTA
7466 CTCTTTA
1 CTCTTTA
*
7473 CTCTTTTT
1 CTC-TTTA
7481 CTCTTTA
1 CTCTTTA
7488 CT
1 CT
7490 AATTACTATT
Statistics
Matches: 329, Mismatches: 88, Indels: 52
0.70 0.19 0.11
Matches are distributed among these distances:
6 2 0.01
7 260 0.79
8 53 0.16
9 11 0.03
10 3 0.01
ACGTcount: A:0.19, C:0.24, G:0.03, T:0.54
Consensus pattern (7 bp):
CTCTTTA
Found at i:7071 original size:77 final size:77
Alignment explanation
Indices: 6873--7085 Score: 358
Period size: 77 Copynumber: 2.8 Consensus size: 77
6863 CTCTTTACTT
* * **
6873 TTTTACCATTTTACCCTTTACTGATTACTCTTTACTCTTTACTAATTACTATTTTACTCTCTTGA
1 TTTTACCATTTTTCTCTTTACTGATTACTCTTTACTCTTTACTCTTTACTATTTTACTCTCTTGA
6938 ATTTAATTACCA
66 ATTTAATTACCA
6950 TTTTACCATTTTTCTCTTTACTGATTACTCTTTACT-TTTAACTCTTTACTATTTTACTCTCTTG
1 TTTTACCATTTTTCTCTTTACTGATTACTCTTTACTCTTT-ACTCTTTACTATTTTACTCTCTTG
7014 AATTTAATTACCA
65 AATTTAATTACCA
*
7027 TTTTACCATTTTTCTCTTTACTGATTACTCTTTACTCTTTACTCTTTACTCTTTT-CTCT
1 TTTTACCATTTTTCTCTTTACTGATTACTCTTTACTCTTTACTCTTTACTATTTTACTCT
7086 TTACTGATTA
Statistics
Matches: 129, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
76 7 0.05
77 119 0.92
78 3 0.02
ACGTcount: A:0.21, C:0.23, G:0.02, T:0.54
Consensus pattern (77 bp):
TTTTACCATTTTTCTCTTTACTGATTACTCTTTACTCTTTACTCTTTACTATTTTACTCTCTTGA
ATTTAATTACCA
Found at i:7338 original size:220 final size:220
Alignment explanation
Indices: 7078--7474 Score: 722
Period size: 220 Copynumber: 1.8 Consensus size: 220
7068 CTCTTTACTC
* *
7078 TTTTCTCTTTACTGATTACTCTATACTCTTTACACTTTTCTCTTTACTGATTACTATATACTGTT
1 TTTTCTCTTTACTGATTACTCTATACTCTTTACACTTTTCTCTTTACTGATAACTATATACTCTT
7143 TACCATTTTCCTCTTTACTGATTACTCTTTACCTTTTACCATTTTACTCTTTACTGATTACTCTT
66 TACCATTTTCCTCTTTACTGATTACTCTTTACCTTTTACCATTTTACTCTTTACTGATTACTCTT
*
7208 TACTTTTTACCATTTTACCCTTTACTGATTACTTTTTACTCTTTACTAATTACTATTTTACTCTC
131 TACTTTTTACCATTTTACCCTTTACTGATTACTCTTTACTCTTTACTAATTACTATTTTACTCTC
7273 TTGAATTTAATTACCATTTTACCAT
196 TTGAATTTAATTACCATTTTACCAT
* *
7298 TTTTCTCTTTACTGATTACTCTATACTCTTTACTCTTTTCTCTTTACTGATAACTCTATACTCTT
1 TTTTCTCTTTACTGATTACTCTATACTCTTTACACTTTTCTCTTTACTGATAACTATATACTCTT
* *
7363 TACCATTTTCCTCTTTACTGTTTACTCTTTACTTTTTACCATTTTACTCTTTACTGATTACTCTT
66 TACCATTTTCCTCTTTACTGATTACTCTTTACCTTTTACCATTTTACTCTTTACTGATTACTCTT
*
7428 TACTTTTTACCATTTTACTCTTTACTGATTACTCTTTACTCTTTACT
131 TACTTTTTACCATTTTACCCTTTACTGATTACTCTTTACTCTTTACT
7475 CTTTTTCTCT
Statistics
Matches: 169, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
220 169 1.00
ACGTcount: A:0.20, C:0.23, G:0.03, T:0.54
Consensus pattern (220 bp):
TTTTCTCTTTACTGATTACTCTATACTCTTTACACTTTTCTCTTTACTGATAACTATATACTCTT
TACCATTTTCCTCTTTACTGATTACTCTTTACCTTTTACCATTTTACTCTTTACTGATTACTCTT
TACTTTTTACCATTTTACCCTTTACTGATTACTCTTTACTCTTTACTAATTACTATTTTACTCTC
TTGAATTTAATTACCATTTTACCAT
Found at i:7495 original size:22 final size:22
Alignment explanation
Indices: 7456--7506 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
7446 TCTTTACTGA
** *
7456 TTACTCTTTACTCTTTACTCTT
1 TTACTCTTTACTAATTACTATT
*
7478 TTTCTCTTTACTAATTACTATT
1 TTACTCTTTACTAATTACTATT
7500 TTACTCT
1 TTACTCT
7507 CTTGATTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.59
Consensus pattern (22 bp):
TTACTCTTTACTAATTACTATT
Found at i:9105 original size:13 final size:13
Alignment explanation
Indices: 9087--9120 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
9077 TAATTATTGT
9087 TTGCTTTATTAAA
1 TTGCTTTATTAAA
*
9100 TTGCTTTATTAAT
1 TTGCTTTATTAAA
9113 TTGCTTTA
1 TTGCTTTA
9121 GATTTGGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.59
Consensus pattern (13 bp):
TTGCTTTATTAAA
Found at i:9136 original size:6 final size:6
Alignment explanation
Indices: 9117--9147 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
9107 ATTAATTTGC
*
9117 TTTAGA TTTGGA TTTAGA TTTAGA TTTAGA T
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA T
9148 CTGCTTTGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (6 bp):
TTTAGA
Found at i:16647 original size:13 final size:13
Alignment explanation
Indices: 16629--16662 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
16619 TAATTATTGT
16629 TTGCTTTATTAAA
1 TTGCTTTATTAAA
*
16642 TTGCTTTATTAAT
1 TTGCTTTATTAAA
16655 TTGCTTTA
1 TTGCTTTA
16663 GATTTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.59
Consensus pattern (13 bp):
TTGCTTTATTAAA
Done.